Nonparametric cellcycleR: Comparison of methods
Kushal K Dey
January 26, 2016
Overview
This script compares the different methods of nonparameteric cellcycleR methods. The aim of the script is to show that the different nonparametric smoothers perform almost equally well as far as the cellcycle ordering is concerned. We consider the same example as in Case Study 4.
Simulation Example
We present a non-sinusoidal gene patterns scenario now.
library(cellcycleR)
library(wavethresh)## Loading required package: MASS
## WaveThresh: R wavelet software, release 4.6.6, installed
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## Copyright Guy Nason and others 1993-2013
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## Note: nlevels has been renamed to nlevelsWTlibrary(binhf)## Loading required package: adlift
## Loading required package: EbayesThresh
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## **********************************************
## adlift: a package to perform wavelet lifting schemes
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## --- Written by Matt Nunes and Marina Knight ---
## Current package version: 1.3-2 ( 01/11/2012 )
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## -+ packaged by MAN +-
## **********************************************
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## adlift 1.3-2 loaded
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## Attaching package: 'adlift'
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## The following object is masked from 'package:EbayesThresh':
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## postmean.cauchy
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## **********************************************
## binhf: Haar-Fisz functions for binomial data
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## --- Written by Matt Nunes ---
## Current package version: 1.0-1 ( 24/04/2014 )
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## **********************************************
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## binhf 1.0-1 loaded
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## Attaching package: 'binhf'
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## The following objects are masked from 'package:EbayesThresh':
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## ebayesthresh.wavelet.wd, negloglik.laplace, wandafromx
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## The following object is masked from 'package:wavethresh':
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## madmad
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## The following object is masked from 'package:base':
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## normG <- 100;
num_cells <- 256;
phi_genes <- seq(1, pi, length.out=G);
sigma_genes <- rchisq(G, 0.01);
cell_times_sim <- sort(sample(seq(0,2*pi, 2*pi/(num_cells-1)), num_cells, replace=FALSE));
cycle_data <- matrix(0,num_cells,G)
base <- c(1:(num_cells/4), (num_cells/4):1, 0.3*(1:(num_cells/4))^2, 0.3*((num_cells/4):1)^2);
for(g in 1:G){
cycle_data[,g] <- rnorm(num_cells,shift(base,2*g, dir="right"),sigma_genes[g]);
}
plot(cycle_data[,1], type="l")
plot(cycle_data[,60], type="l")
plot(cycle_data[,30], type="l")
celltime_levels <- 256;
sample_reorder <- sample(1:num_cells,num_cells, replace=FALSE);
cell_times_reorder <- cell_times_sim[sample_reorder];
cycle_data_reorder <- cycle_data[sample_reorder,];Nonparametric cellcycleR : LOESS method
system.time(out_np <- np_cell_ordering_class(cycle_data_reorder, celltime_levels = 256, num_iter=500, method="LOESS"))## The loglikelihood after iter 1 is: -182365.804952
## The loglikelihood after iter 2 is: -176884.811244
## The loglikelihood after iter 3 is: -175630.864697
## The loglikelihood after iter 4 is: -176284.396326
## The loglikelihood after iter 5 is: -176297.073452
## The loglikelihood after iter 6 is: -176605.527124
## The loglikelihood after iter 7 is: -176694.891786
## The loglikelihood after iter 8 is: -176979.361584
## The loglikelihood after iter 9 is: -176907.323388
## The loglikelihood after iter 10 is: -176612.38812
## The loglikelihood after iter 11 is: -176891.761598
## The loglikelihood after iter 12 is: -176838.861791
## The loglikelihood after iter 13 is: -176985.151184
## The loglikelihood after iter 14 is: -177289.538847
## The loglikelihood after iter 15 is: -177193.963971
## The loglikelihood after iter 16 is: -177180.921727
## The loglikelihood after iter 17 is: -177148.319244
## The loglikelihood after iter 18 is: -177051.825007
## The loglikelihood after iter 19 is: -176721.818003
## The loglikelihood after iter 20 is: -176403.819568
## The loglikelihood after iter 21 is: -175792.853722
## The loglikelihood after iter 22 is: -175407.986673
## The loglikelihood after iter 23 is: -175168.324097
## The loglikelihood after iter 24 is: -175120.235424
## The loglikelihood after iter 25 is: -175080.067776
## The loglikelihood after iter 26 is: -175014.9034
## The loglikelihood after iter 27 is: -175005.732909
## The loglikelihood after iter 28 is: -174934.697802
## The loglikelihood after iter 29 is: -175012.76655
## The loglikelihood after iter 30 is: -174990.492272
## The loglikelihood after iter 31 is: -175047.084832
## The loglikelihood after iter 32 is: -175137.971536
## The loglikelihood after iter 33 is: -175218.127631
## The loglikelihood after iter 34 is: -175533.270256
## The loglikelihood after iter 35 is: -175699.70117
## The loglikelihood after iter 36 is: -175936.269356
## The loglikelihood after iter 37 is: -176257.800344
## The loglikelihood after iter 38 is: -176169.120664
## The loglikelihood after iter 39 is: -175103.585749
## The loglikelihood after iter 40 is: -175011.394691
## The loglikelihood after iter 41 is: -175062.158602
## The loglikelihood after iter 42 is: -175016.377963
## The loglikelihood after iter 43 is: -174905.348437
## The loglikelihood after iter 44 is: -175279.838451
## The loglikelihood after iter 45 is: -175345.18683
## The loglikelihood after iter 46 is: -175347.670732
## The loglikelihood after iter 47 is: -175495.997132
## The loglikelihood after iter 48 is: -175522.176496
## The loglikelihood after iter 49 is: -175688.079039
## The loglikelihood after iter 50 is: -175973.332853
## The loglikelihood after iter 51 is: -175635.769323
## The loglikelihood after iter 52 is: -176142.75127
## The loglikelihood after iter 53 is: -176197.386022
## The loglikelihood after iter 54 is: -175734.489076
## The loglikelihood after iter 55 is: -175924.875108
## The loglikelihood after iter 56 is: -176057.333855
## The loglikelihood after iter 57 is: -176099.5076
## The loglikelihood after iter 58 is: -176090.255551
## The loglikelihood after iter 59 is: -175853.849452
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## The loglikelihood after iter 62 is: -176543.294253
## The loglikelihood after iter 63 is: -176351.440515
## The loglikelihood after iter 64 is: -176576.678353
## The loglikelihood after iter 65 is: -176397.144118
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## The loglikelihood after iter 68 is: -176875.259234
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## The loglikelihood after iter 75 is: -176492.729794
## The loglikelihood after iter 76 is: -177320.60388
## The loglikelihood after iter 77 is: -176598.943782
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## The loglikelihood after iter 108 is: -177296.210785
## The loglikelihood after iter 109 is: -176716.472052
## The loglikelihood after iter 110 is: -177589.150215
## The loglikelihood after iter 111 is: -176781.186132
## The loglikelihood after iter 112 is: -177196.880581
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## The loglikelihood after iter 122 is: -177443.211867
## The loglikelihood after iter 123 is: -176686.145592
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## The loglikelihood after iter 128 is: -177546.50262
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## The loglikelihood after iter 130 is: -176629.754539
## The loglikelihood after iter 131 is: -176630.615282
## The loglikelihood after iter 132 is: -176399.878489
## The loglikelihood after iter 133 is: -176804.830205
## The loglikelihood after iter 134 is: -176736.300415
## The loglikelihood after iter 135 is: -177220.935085
## The loglikelihood after iter 136 is: -177071.729059
## The loglikelihood after iter 137 is: -176866.612807
## The loglikelihood after iter 138 is: -177494.877397
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## The loglikelihood after iter 140 is: -176875.603642
## The loglikelihood after iter 141 is: -176913.54699
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## The loglikelihood after iter 143 is: -177419.552243
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## The loglikelihood after iter 146 is: -177084.102403
## The loglikelihood after iter 147 is: -177035.713104
## The loglikelihood after iter 148 is: -177041.895745
## The loglikelihood after iter 149 is: -176594.48614
## The loglikelihood after iter 150 is: -177483.060193
## The loglikelihood after iter 151 is: -177718.329033
## The loglikelihood after iter 152 is: -177040.559777
## The loglikelihood after iter 153 is: -177581.775318
## The loglikelihood after iter 154 is: -177109.336658
## The loglikelihood after iter 155 is: -177571.879577
## The loglikelihood after iter 156 is: -176563.365262
## The loglikelihood after iter 157 is: -177753.308606
## The loglikelihood after iter 158 is: -176403.320992
## The loglikelihood after iter 159 is: -176525.829625
## The loglikelihood after iter 160 is: -177132.559751
## The loglikelihood after iter 161 is: -176651.64705
## The loglikelihood after iter 162 is: -176728.068582
## The loglikelihood after iter 163 is: -176981.165062
## The loglikelihood after iter 164 is: -176762.548137
## The loglikelihood after iter 165 is: -176831.177093
## The loglikelihood after iter 166 is: -177212.008744
## The loglikelihood after iter 167 is: -177209.687128
## The loglikelihood after iter 168 is: -176765.841919
## The loglikelihood after iter 169 is: -177670.463013
## The loglikelihood after iter 170 is: -176479.930833
## The loglikelihood after iter 171 is: -177657.529596
## The loglikelihood after iter 172 is: -176520.620765
## The loglikelihood after iter 173 is: -177358.932284
## The loglikelihood after iter 174 is: -176696.391687
## The loglikelihood after iter 175 is: -176604.557178
## The loglikelihood after iter 176 is: -177429.699989
## The loglikelihood after iter 177 is: -176550.469398
## The loglikelihood after iter 178 is: -177166.287206
## The loglikelihood after iter 179 is: -176757.031026
## The loglikelihood after iter 180 is: -176387.178794
## The loglikelihood after iter 181 is: -176841.455445
## The loglikelihood after iter 182 is: -176317.569999
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## The loglikelihood after iter 188 is: -176554.256047
## The loglikelihood after iter 189 is: -176829.868774
## The loglikelihood after iter 190 is: -176705.650992
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## The loglikelihood after iter 193 is: -177276.422162
## The loglikelihood after iter 194 is: -176760.402194
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## The loglikelihood after iter 196 is: -176808.985887
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## The loglikelihood after iter 200 is: -176846.91597
## The loglikelihood after iter 201 is: -176839.080497
## The loglikelihood after iter 202 is: -177067.215777
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## The loglikelihood after iter 208 is: -176516.026262
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## The loglikelihood after iter 215 is: -176476.657022
## The loglikelihood after iter 216 is: -177346.505302
## The loglikelihood after iter 217 is: -176752.470773
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## The loglikelihood after iter 219 is: -176998.495505
## The loglikelihood after iter 220 is: -177139.483213
## The loglikelihood after iter 221 is: -177428.066672
## The loglikelihood after iter 222 is: -177135.684757
## The loglikelihood after iter 223 is: -176782.971677
## The loglikelihood after iter 224 is: -177134.949968
## The loglikelihood after iter 225 is: -177616.973942
## The loglikelihood after iter 226 is: -176652.929842
## The loglikelihood after iter 227 is: -177670.648141
## The loglikelihood after iter 228 is: -176701.800568
## The loglikelihood after iter 229 is: -177173.979067
## The loglikelihood after iter 230 is: -177479.225362
## The loglikelihood after iter 231 is: -177092.400854
## The loglikelihood after iter 232 is: -177365.720546
## The loglikelihood after iter 233 is: -177351.439376
## The loglikelihood after iter 234 is: -176919.642294
## The loglikelihood after iter 235 is: -177548.34468
## The loglikelihood after iter 236 is: -177105.781495
## The loglikelihood after iter 237 is: -177005.960236
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## The loglikelihood after iter 242 is: -177410.030611
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## The loglikelihood after iter 245 is: -177882.845819
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## The loglikelihood after iter 247 is: -177480.914548
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## The loglikelihood after iter 249 is: -176686.099372
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## The loglikelihood after iter 253 is: -176420.645267
## The loglikelihood after iter 254 is: -177170.592406
## The loglikelihood after iter 255 is: -177056.639284
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## The loglikelihood after iter 260 is: -177104.629802
## The loglikelihood after iter 261 is: -177034.053641
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## The loglikelihood after iter 275 is: -176777.137617
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## The loglikelihood after iter 280 is: -176896.974877
## The loglikelihood after iter 281 is: -177225.338706
## The loglikelihood after iter 282 is: -176626.980031
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## The loglikelihood after iter 285 is: -177357.34439
## The loglikelihood after iter 286 is: -177631.481993
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## The loglikelihood after iter 289 is: -176995.579588
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## The loglikelihood after iter 291 is: -177029.064342
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## The loglikelihood after iter 379 is: -176678.039953
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## The loglikelihood after iter 381 is: -176670.712333
## The loglikelihood after iter 382 is: -177327.400375
## The loglikelihood after iter 383 is: -176551.670282
## The loglikelihood after iter 384 is: -177448.937571
## The loglikelihood after iter 385 is: -176353.391393
## The loglikelihood after iter 386 is: -177097.911492
## The loglikelihood after iter 387 is: -176890.101541
## The loglikelihood after iter 388 is: -177056.835183
## The loglikelihood after iter 389 is: -176310.580357
## The loglikelihood after iter 390 is: -177015.098945
## The loglikelihood after iter 391 is: -176744.370171
## The loglikelihood after iter 392 is: -176760.920836
## The loglikelihood after iter 393 is: -176806.766521
## The loglikelihood after iter 394 is: -176908.862248
## The loglikelihood after iter 395 is: -176722.485608
## The loglikelihood after iter 396 is: -177194.914511
## The loglikelihood after iter 397 is: -176434.93308
## The loglikelihood after iter 398 is: -177016.755909
## The loglikelihood after iter 399 is: -176686.43104
## The loglikelihood after iter 400 is: -177193.827078
## The loglikelihood after iter 401 is: -177330.857036
## The loglikelihood after iter 402 is: -176345.997603
## The loglikelihood after iter 403 is: -177571.360286
## The loglikelihood after iter 404 is: -176317.849724
## The loglikelihood after iter 405 is: -177101.330356
## The loglikelihood after iter 406 is: -176342.289629
## The loglikelihood after iter 407 is: -177434.525076
## The loglikelihood after iter 408 is: -176646.561764
## The loglikelihood after iter 409 is: -177098.498662
## The loglikelihood after iter 410 is: -176865.628551
## The loglikelihood after iter 411 is: -176858.219625
## The loglikelihood after iter 412 is: -177126.750591
## The loglikelihood after iter 413 is: -176766.750134
## The loglikelihood after iter 414 is: -176967.133605
## The loglikelihood after iter 415 is: -176470.203235
## The loglikelihood after iter 416 is: -177253.102339
## The loglikelihood after iter 417 is: -176692.893263
## The loglikelihood after iter 418 is: -177045.03022
## The loglikelihood after iter 419 is: -177108.028993
## The loglikelihood after iter 420 is: -177237.391403
## The loglikelihood after iter 421 is: -176901.378403
## The loglikelihood after iter 422 is: -177346.666576
## The loglikelihood after iter 423 is: -176787.11213
## The loglikelihood after iter 424 is: -177312.263953
## The loglikelihood after iter 425 is: -177107.303938
## The loglikelihood after iter 426 is: -177446.668651
## The loglikelihood after iter 427 is: -176987.975573
## The loglikelihood after iter 428 is: -177113.475852
## The loglikelihood after iter 429 is: -177339.240595
## The loglikelihood after iter 430 is: -177066.214942
## The loglikelihood after iter 431 is: -177526.127579
## The loglikelihood after iter 432 is: -177160.394659
## The loglikelihood after iter 433 is: -177434.622742
## The loglikelihood after iter 434 is: -176832.682256
## The loglikelihood after iter 435 is: -177163.965113
## The loglikelihood after iter 436 is: -177007.342901
## The loglikelihood after iter 437 is: -176522.276463
## The loglikelihood after iter 438 is: -177738.699667
## The loglikelihood after iter 439 is: -177126.235388
## The loglikelihood after iter 440 is: -177246.812598
## The loglikelihood after iter 441 is: -177860.803462
## The loglikelihood after iter 442 is: -177064.80834
## The loglikelihood after iter 443 is: -177983.58879
## The loglikelihood after iter 444 is: -177019.808528
## The loglikelihood after iter 445 is: -177749.633093
## The loglikelihood after iter 446 is: -177045.922175
## The loglikelihood after iter 447 is: -177043.037784
## The loglikelihood after iter 448 is: -177731.130775
## The loglikelihood after iter 449 is: -176867.813437
## The loglikelihood after iter 450 is: -177288.889795
## The loglikelihood after iter 451 is: -176556.951024
## The loglikelihood after iter 452 is: -176796.00619
## The loglikelihood after iter 453 is: -176744.018688
## The loglikelihood after iter 454 is: -176284.586483
## The loglikelihood after iter 455 is: -176568.988395
## The loglikelihood after iter 456 is: -176791.477841
## The loglikelihood after iter 457 is: -176740.416788
## The loglikelihood after iter 458 is: -176967.760726
## The loglikelihood after iter 459 is: -176871.338117
## The loglikelihood after iter 460 is: -177129.117299
## The loglikelihood after iter 461 is: -177310.85696
## The loglikelihood after iter 462 is: -176564.937136
## The loglikelihood after iter 463 is: -177588.444375
## The loglikelihood after iter 464 is: -177251.955057
## The loglikelihood after iter 465 is: -177504.214513
## The loglikelihood after iter 466 is: -177328.890996
## The loglikelihood after iter 467 is: -177969.462068
## The loglikelihood after iter 468 is: -176754.397783
## The loglikelihood after iter 469 is: -178084.292968
## The loglikelihood after iter 470 is: -176822.350075
## The loglikelihood after iter 471 is: -177589.705069
## The loglikelihood after iter 472 is: -177330.485634
## The loglikelihood after iter 473 is: -177749.516534
## The loglikelihood after iter 474 is: -176623.029167
## The loglikelihood after iter 475 is: -177772.106663
## The loglikelihood after iter 476 is: -176534.997221
## The loglikelihood after iter 477 is: -177224.417698
## The loglikelihood after iter 478 is: -176799.775689
## The loglikelihood after iter 479 is: -177197.594034
## The loglikelihood after iter 480 is: -176698.620297
## The loglikelihood after iter 481 is: -177149.518598
## The loglikelihood after iter 482 is: -177264.392079
## The loglikelihood after iter 483 is: -177091.991568
## The loglikelihood after iter 484 is: -177281.703651
## The loglikelihood after iter 485 is: -177505.234177
## The loglikelihood after iter 486 is: -177044.782859
## The loglikelihood after iter 487 is: -177308.015806
## The loglikelihood after iter 488 is: -176771.003595
## The loglikelihood after iter 489 is: -177688.713114
## The loglikelihood after iter 490 is: -176640.605203
## The loglikelihood after iter 491 is: -177041.725439
## The loglikelihood after iter 492 is: -176732.469992
## The loglikelihood after iter 493 is: -177301.723331
## The loglikelihood after iter 494 is: -177045.740017
## The loglikelihood after iter 495 is: -176841.400268
## The loglikelihood after iter 496 is: -177045.888455
## The loglikelihood after iter 497 is: -176899.504966
## The loglikelihood after iter 498 is: -177397.607523
## The loglikelihood after iter 499 is: -177192.85755
## The loglikelihood after iter 500 is: -177363.045305## user system elapsed
## 1169.063 297.826 469.182library(plotrix)## Warning: package 'plotrix' was built under R version 3.2.3library(RColorBrewer)
radial.plot(lengths=1:length(out_np$cell_times),radial.pos=out_np$cell_times[order(cell_times_reorder)],
line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(out_np$cell_times)), lwd=2)
radial.plot(lengths=1:length(cell_times_reorder),radial.pos=sort(cell_times_reorder),
line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(cell_times_reorder)), lwd=2)
The plots of estimated gene pattern and the true gene pattern.
First co-ordinate
plot(cycle_data_reorder[order(out_np$cell_times),1], type="l")
plot(cycle_data[,1],type="l")
30th coordinate
plot(cycle_data_reorder[order(out_np$cell_times),30], type="l")
plot(cycle_data[,30],type="l")
50th coordinate
plot(cycle_data_reorder[order(out_np$cell_times),50], type="l")
plot(cycle_data[,50],type="l")
Nonparametric cellcycleR : B-spline method
system.time(out_np <- np_cell_ordering_class(cycle_data_reorder, celltime_levels = 256, num_iter=500, method="B-spline"))## The loglikelihood after iter 1 is: -182162.046669
## The loglikelihood after iter 2 is: -176829.917174
## The loglikelihood after iter 3 is: -176521.898403
## The loglikelihood after iter 4 is: -176168.953658
## The loglikelihood after iter 5 is: -176264.932377
## The loglikelihood after iter 6 is: -176455.637098
## The loglikelihood after iter 7 is: -176672.668228
## The loglikelihood after iter 8 is: -176469.712431
## The loglikelihood after iter 9 is: -176851.584573
## The loglikelihood after iter 10 is: -176808.367671
## The loglikelihood after iter 11 is: -176709.596945
## The loglikelihood after iter 12 is: -176862.866977
## The loglikelihood after iter 13 is: -176827.76757
## The loglikelihood after iter 14 is: -176688.83508
## The loglikelihood after iter 15 is: -176877.759329
## The loglikelihood after iter 16 is: -176923.270499
## The loglikelihood after iter 17 is: -176886.105347
## The loglikelihood after iter 18 is: -177012.255356
## The loglikelihood after iter 19 is: -176856.648728
## The loglikelihood after iter 20 is: -176948.076141
## The loglikelihood after iter 21 is: -177004.807622
## The loglikelihood after iter 22 is: -177340.841678
## The loglikelihood after iter 23 is: -176745.657544
## The loglikelihood after iter 24 is: -177087.920162
## The loglikelihood after iter 25 is: -176805.126478
## The loglikelihood after iter 26 is: -176784.976435
## The loglikelihood after iter 27 is: -176438.541996
## The loglikelihood after iter 28 is: -176813.639299
## The loglikelihood after iter 29 is: -176672.505141
## The loglikelihood after iter 30 is: -176630.104203
## The loglikelihood after iter 31 is: -176370.208704
## The loglikelihood after iter 32 is: -176384.450639
## The loglikelihood after iter 33 is: -176167.40294
## The loglikelihood after iter 34 is: -175718.251154
## The loglikelihood after iter 35 is: -175352.12369
## The loglikelihood after iter 36 is: -175263.989825
## The loglikelihood after iter 37 is: -175113.314427
## The loglikelihood after iter 38 is: -175210.157071
## The loglikelihood after iter 39 is: -175184.452848
## The loglikelihood after iter 40 is: -175353.118798
## The loglikelihood after iter 41 is: -175456.585089
## The loglikelihood after iter 42 is: -175494.741611
## The loglikelihood after iter 43 is: -175560.077612
## The loglikelihood after iter 44 is: -175560.16175
## The loglikelihood after iter 45 is: -175225.484516
## The loglikelihood after iter 46 is: -174364.334856
## The loglikelihood after iter 47 is: -174313.336306
## The loglikelihood after iter 48 is: -174260.047439
## The loglikelihood after iter 49 is: -174239.330431
## The loglikelihood after iter 50 is: -174269.636284
## The loglikelihood after iter 51 is: -174392.577478
## The loglikelihood after iter 52 is: -174425.495884
## The loglikelihood after iter 53 is: -174496.727835
## The loglikelihood after iter 54 is: -174651.356133
## The loglikelihood after iter 55 is: -174741.741102
## The loglikelihood after iter 56 is: -174822.22445
## The loglikelihood after iter 57 is: -174822.758001
## The loglikelihood after iter 58 is: -175103.760703
## The loglikelihood after iter 59 is: -175075.895252
## The loglikelihood after iter 60 is: -175153.799151
## The loglikelihood after iter 61 is: -175261.331793
## The loglikelihood after iter 62 is: -175423.991512
## The loglikelihood after iter 63 is: -175344.422292
## The loglikelihood after iter 64 is: -175631.131982
## The loglikelihood after iter 65 is: -175679.841832
## The loglikelihood after iter 66 is: -175607.459551
## The loglikelihood after iter 67 is: -175843.399784
## The loglikelihood after iter 68 is: -175667.465939
## The loglikelihood after iter 69 is: -176142.320734
## The loglikelihood after iter 70 is: -176178.693669
## The loglikelihood after iter 71 is: -176238.791542
## The loglikelihood after iter 72 is: -176278.242149
## The loglikelihood after iter 73 is: -176494.296492
## The loglikelihood after iter 74 is: -176389.777077
## The loglikelihood after iter 75 is: -176469.089689
## The loglikelihood after iter 76 is: -176438.315554
## The loglikelihood after iter 77 is: -176384.138213
## The loglikelihood after iter 78 is: -176562.423186
## The loglikelihood after iter 79 is: -176426.712005
## The loglikelihood after iter 80 is: -176559.174731
## The loglikelihood after iter 81 is: -176539.344299
## The loglikelihood after iter 82 is: -176807.294683
## The loglikelihood after iter 83 is: -176542.0427
## The loglikelihood after iter 84 is: -176741.468139
## The loglikelihood after iter 85 is: -176736.416858
## The loglikelihood after iter 86 is: -176812.749206
## The loglikelihood after iter 87 is: -176990.947102
## The loglikelihood after iter 88 is: -176722.627554
## The loglikelihood after iter 89 is: -176940.978295
## The loglikelihood after iter 90 is: -177024.238506
## The loglikelihood after iter 91 is: -176949.585441
## The loglikelihood after iter 92 is: -176985.289313
## The loglikelihood after iter 93 is: -176889.115182
## The loglikelihood after iter 94 is: -177018.092216
## The loglikelihood after iter 95 is: -177365.961787
## The loglikelihood after iter 96 is: -176921.573578
## The loglikelihood after iter 97 is: -177359.858076
## The loglikelihood after iter 98 is: -177128.040114
## The loglikelihood after iter 99 is: -177094.809467
## The loglikelihood after iter 100 is: -177094.298744
## The loglikelihood after iter 101 is: -177177.340207
## The loglikelihood after iter 102 is: -177312.91597
## The loglikelihood after iter 103 is: -176941.397942
## The loglikelihood after iter 104 is: -177249.592179
## The loglikelihood after iter 105 is: -177252.856133
## The loglikelihood after iter 106 is: -177154.766991
## The loglikelihood after iter 107 is: -177247.436146
## The loglikelihood after iter 108 is: -177246.036136
## The loglikelihood after iter 109 is: -177260.85813
## The loglikelihood after iter 110 is: -177177.302405
## The loglikelihood after iter 111 is: -177313.811295
## The loglikelihood after iter 112 is: -177228.664134
## The loglikelihood after iter 113 is: -177091.709977
## The loglikelihood after iter 114 is: -177342.958077
## The loglikelihood after iter 115 is: -176967.126345
## The loglikelihood after iter 116 is: -177429.754886
## The loglikelihood after iter 117 is: -176921.901435
## The loglikelihood after iter 118 is: -177009.006598
## The loglikelihood after iter 119 is: -176882.070423
## The loglikelihood after iter 120 is: -176835.810919
## The loglikelihood after iter 121 is: -176809.62085
## The loglikelihood after iter 122 is: -177181.332961
## The loglikelihood after iter 123 is: -176481.336605
## The loglikelihood after iter 124 is: -176903.549543
## The loglikelihood after iter 125 is: -176696.735527
## The loglikelihood after iter 126 is: -176700.223635
## The loglikelihood after iter 127 is: -176835.826056
## The loglikelihood after iter 128 is: -176819.543636
## The loglikelihood after iter 129 is: -176715.53063
## The loglikelihood after iter 130 is: -176710.403836
## The loglikelihood after iter 131 is: -176848.545597
## The loglikelihood after iter 132 is: -176453.310838
## The loglikelihood after iter 133 is: -176992.55898
## The loglikelihood after iter 134 is: -176657.908872
## The loglikelihood after iter 135 is: -176649.101977
## The loglikelihood after iter 136 is: -176696.271765
## The loglikelihood after iter 137 is: -176667.661939
## The loglikelihood after iter 138 is: -176526.214321
## The loglikelihood after iter 139 is: -176693.793199
## The loglikelihood after iter 140 is: -176610.511655
## The loglikelihood after iter 141 is: -176697.88115
## The loglikelihood after iter 142 is: -176836.727519
## The loglikelihood after iter 143 is: -176821.340026
## The loglikelihood after iter 144 is: -176532.591875
## The loglikelihood after iter 145 is: -176872.300796
## The loglikelihood after iter 146 is: -176698.428685
## The loglikelihood after iter 147 is: -176796.269344
## The loglikelihood after iter 148 is: -176646.349914
## The loglikelihood after iter 149 is: -176729.493733
## The loglikelihood after iter 150 is: -176748.119864
## The loglikelihood after iter 151 is: -176767.887289
## The loglikelihood after iter 152 is: -176841.176674
## The loglikelihood after iter 153 is: -176754.302331
## The loglikelihood after iter 154 is: -176720.948427
## The loglikelihood after iter 155 is: -176789.588592
## The loglikelihood after iter 156 is: -176716.140773
## The loglikelihood after iter 157 is: -176673.6284
## The loglikelihood after iter 158 is: -176671.623364
## The loglikelihood after iter 159 is: -176741.523973
## The loglikelihood after iter 160 is: -176722.449236
## The loglikelihood after iter 161 is: -176803.03316
## The loglikelihood after iter 162 is: -176769.797951
## The loglikelihood after iter 163 is: -177012.268944
## The loglikelihood after iter 164 is: -176758.854655
## The loglikelihood after iter 165 is: -177100.066402
## The loglikelihood after iter 166 is: -177039.202202
## The loglikelihood after iter 167 is: -176904.345446
## The loglikelihood after iter 168 is: -176899.775459
## The loglikelihood after iter 169 is: -176757.954264
## The loglikelihood after iter 170 is: -176827.573565
## The loglikelihood after iter 171 is: -176719.87025
## The loglikelihood after iter 172 is: -176993.731999
## The loglikelihood after iter 173 is: -176643.030229
## The loglikelihood after iter 174 is: -176852.711688
## The loglikelihood after iter 175 is: -176684.869977
## The loglikelihood after iter 176 is: -176770.088758
## The loglikelihood after iter 177 is: -176750.727622
## The loglikelihood after iter 178 is: -176616.918216
## The loglikelihood after iter 179 is: -176733.550125
## The loglikelihood after iter 180 is: -176707.553455
## The loglikelihood after iter 181 is: -176780.768673
## The loglikelihood after iter 182 is: -176649.677508
## The loglikelihood after iter 183 is: -176567.390357
## The loglikelihood after iter 184 is: -176610.943388
## The loglikelihood after iter 185 is: -176727.212326
## The loglikelihood after iter 186 is: -176388.697858
## The loglikelihood after iter 187 is: -176804.226751
## The loglikelihood after iter 188 is: -176732.373522
## The loglikelihood after iter 189 is: -176945.632001
## The loglikelihood after iter 190 is: -176701.13446
## The loglikelihood after iter 191 is: -176847.202685
## The loglikelihood after iter 192 is: -176801.951018
## The loglikelihood after iter 193 is: -176711.001094
## The loglikelihood after iter 194 is: -176719.976008
## The loglikelihood after iter 195 is: -176758.581936
## The loglikelihood after iter 196 is: -176644.259058
## The loglikelihood after iter 197 is: -176807.307192
## The loglikelihood after iter 198 is: -176664.450793
## The loglikelihood after iter 199 is: -176738.495507
## The loglikelihood after iter 200 is: -176897.145678
## The loglikelihood after iter 201 is: -176879.005063
## The loglikelihood after iter 202 is: -176842.448393
## The loglikelihood after iter 203 is: -176797.795738
## The loglikelihood after iter 204 is: -176893.896427
## The loglikelihood after iter 205 is: -176864.468733
## The loglikelihood after iter 206 is: -176793.39345
## The loglikelihood after iter 207 is: -176958.818295
## The loglikelihood after iter 208 is: -176682.04756
## The loglikelihood after iter 209 is: -176756.652819
## The loglikelihood after iter 210 is: -176778.730437
## The loglikelihood after iter 211 is: -176685.217588
## The loglikelihood after iter 212 is: -176804.554324
## The loglikelihood after iter 213 is: -176737.868414
## The loglikelihood after iter 214 is: -176831.800802
## The loglikelihood after iter 215 is: -176815.633004
## The loglikelihood after iter 216 is: -176854.327057
## The loglikelihood after iter 217 is: -176801.19921
## The loglikelihood after iter 218 is: -176868.522744
## The loglikelihood after iter 219 is: -176893.346987
## The loglikelihood after iter 220 is: -176827.679565
## The loglikelihood after iter 221 is: -176825.475467
## The loglikelihood after iter 222 is: -176734.10552
## The loglikelihood after iter 223 is: -176688.907182
## The loglikelihood after iter 224 is: -176618.854444
## The loglikelihood after iter 225 is: -176660.836614
## The loglikelihood after iter 226 is: -176610.43455
## The loglikelihood after iter 227 is: -176727.628093
## The loglikelihood after iter 228 is: -176736.507628
## The loglikelihood after iter 229 is: -176710.712451
## The loglikelihood after iter 230 is: -176654.379794
## The loglikelihood after iter 231 is: -176627.02709
## The loglikelihood after iter 232 is: -176591.056957
## The loglikelihood after iter 233 is: -176644.146007
## The loglikelihood after iter 234 is: -176737.458031
## The loglikelihood after iter 235 is: -176704.999969
## The loglikelihood after iter 236 is: -176719.304203
## The loglikelihood after iter 237 is: -176907.065489
## The loglikelihood after iter 238 is: -176818.838654
## The loglikelihood after iter 239 is: -176903.870705
## The loglikelihood after iter 240 is: -176903.651195
## The loglikelihood after iter 241 is: -176916.423337
## The loglikelihood after iter 242 is: -176737.452133
## The loglikelihood after iter 243 is: -176761.034734
## The loglikelihood after iter 244 is: -176972.768872
## The loglikelihood after iter 245 is: -176863.687177
## The loglikelihood after iter 246 is: -176801.566762
## The loglikelihood after iter 247 is: -176996.951456
## The loglikelihood after iter 248 is: -176842.297676
## The loglikelihood after iter 249 is: -176854.986575
## The loglikelihood after iter 250 is: -177001.201546
## The loglikelihood after iter 251 is: -177032.760589
## The loglikelihood after iter 252 is: -176957.08517
## The loglikelihood after iter 253 is: -176975.038418
## The loglikelihood after iter 254 is: -176913.686047
## The loglikelihood after iter 255 is: -176925.197724
## The loglikelihood after iter 256 is: -176930.527235
## The loglikelihood after iter 257 is: -176991.816359
## The loglikelihood after iter 258 is: -176989.155895
## The loglikelihood after iter 259 is: -177083.83202
## The loglikelihood after iter 260 is: -176989.542294
## The loglikelihood after iter 261 is: -177050.408955
## The loglikelihood after iter 262 is: -176965.029639
## The loglikelihood after iter 263 is: -177028.548271
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## The loglikelihood after iter 266 is: -176957.828093
## The loglikelihood after iter 267 is: -176791.332093
## The loglikelihood after iter 268 is: -176797.819576
## The loglikelihood after iter 269 is: -177034.036343
## The loglikelihood after iter 270 is: -177009.549815
## The loglikelihood after iter 271 is: -176928.086715
## The loglikelihood after iter 272 is: -176994.944013
## The loglikelihood after iter 273 is: -176927.002269
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## The loglikelihood after iter 275 is: -176940.728806
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## The loglikelihood after iter 283 is: -176882.205621
## The loglikelihood after iter 284 is: -177124.557156
## The loglikelihood after iter 285 is: -176879.033514
## The loglikelihood after iter 286 is: -176864.484834
## The loglikelihood after iter 287 is: -176941.489789
## The loglikelihood after iter 288 is: -177079.605442
## The loglikelihood after iter 289 is: -177087.531989
## The loglikelihood after iter 290 is: -176953.461892
## The loglikelihood after iter 291 is: -176872.51757
## The loglikelihood after iter 292 is: -176775.110109
## The loglikelihood after iter 293 is: -176857.621575
## The loglikelihood after iter 294 is: -176933.875717
## The loglikelihood after iter 295 is: -176766.598608
## The loglikelihood after iter 296 is: -176939.903478
## The loglikelihood after iter 297 is: -176954.659506
## The loglikelihood after iter 298 is: -176955.599535
## The loglikelihood after iter 299 is: -176854.658109
## The loglikelihood after iter 300 is: -176849.13663
## The loglikelihood after iter 301 is: -176918.003066
## The loglikelihood after iter 302 is: -176856.164674
## The loglikelihood after iter 303 is: -176942.342636
## The loglikelihood after iter 304 is: -176732.952846
## The loglikelihood after iter 305 is: -176881.436331
## The loglikelihood after iter 306 is: -176670.878787
## The loglikelihood after iter 307 is: -176706.011418
## The loglikelihood after iter 308 is: -176710.541065
## The loglikelihood after iter 309 is: -176816.598902
## The loglikelihood after iter 310 is: -176660.113605
## The loglikelihood after iter 311 is: -176738.729876
## The loglikelihood after iter 312 is: -176802.885364
## The loglikelihood after iter 313 is: -176858.408059
## The loglikelihood after iter 314 is: -176821.108099
## The loglikelihood after iter 315 is: -176611.866167
## The loglikelihood after iter 316 is: -176756.017011
## The loglikelihood after iter 317 is: -176873.504742
## The loglikelihood after iter 318 is: -176976.660659
## The loglikelihood after iter 319 is: -176805.955888
## The loglikelihood after iter 320 is: -176861.81175
## The loglikelihood after iter 321 is: -176775.833507
## The loglikelihood after iter 322 is: -176780.805767
## The loglikelihood after iter 323 is: -176899.203877
## The loglikelihood after iter 324 is: -176818.244819
## The loglikelihood after iter 325 is: -176776.807622
## The loglikelihood after iter 326 is: -176846.863533
## The loglikelihood after iter 327 is: -176785.899315
## The loglikelihood after iter 328 is: -176823.884913
## The loglikelihood after iter 329 is: -176789.631547
## The loglikelihood after iter 330 is: -176646.762244
## The loglikelihood after iter 331 is: -176660.89919
## The loglikelihood after iter 332 is: -176689.619039
## The loglikelihood after iter 333 is: -176812.494941
## The loglikelihood after iter 334 is: -176821.816618
## The loglikelihood after iter 335 is: -176793.931003
## The loglikelihood after iter 336 is: -176713.393659
## The loglikelihood after iter 337 is: -176813.643807
## The loglikelihood after iter 338 is: -176735.547856
## The loglikelihood after iter 339 is: -176877.29618
## The loglikelihood after iter 340 is: -176804.377825
## The loglikelihood after iter 341 is: -176890.903544
## The loglikelihood after iter 342 is: -176816.017143
## The loglikelihood after iter 343 is: -176734.695824
## The loglikelihood after iter 344 is: -176715.323339
## The loglikelihood after iter 345 is: -176805.620698
## The loglikelihood after iter 346 is: -176878.381187
## The loglikelihood after iter 347 is: -176890.53384
## The loglikelihood after iter 348 is: -176894.984747
## The loglikelihood after iter 349 is: -177099.99496
## The loglikelihood after iter 350 is: -177039.982695
## The loglikelihood after iter 351 is: -177016.009143
## The loglikelihood after iter 352 is: -176905.003315
## The loglikelihood after iter 353 is: -176920.82917
## The loglikelihood after iter 354 is: -176866.733589
## The loglikelihood after iter 355 is: -177030.096942
## The loglikelihood after iter 356 is: -176903.878255
## The loglikelihood after iter 357 is: -176980.416777
## The loglikelihood after iter 358 is: -176901.949112
## The loglikelihood after iter 359 is: -176950.944254
## The loglikelihood after iter 360 is: -176917.798941
## The loglikelihood after iter 361 is: -177083.104221
## The loglikelihood after iter 362 is: -176935.399646
## The loglikelihood after iter 363 is: -177024.485102
## The loglikelihood after iter 364 is: -176965.735433
## The loglikelihood after iter 365 is: -177040.895062
## The loglikelihood after iter 366 is: -177136.954445
## The loglikelihood after iter 367 is: -176906.285899
## The loglikelihood after iter 368 is: -176981.491501
## The loglikelihood after iter 369 is: -177119.409761
## The loglikelihood after iter 370 is: -177135.894685
## The loglikelihood after iter 371 is: -177194.010235
## The loglikelihood after iter 372 is: -177083.201808
## The loglikelihood after iter 373 is: -177113.632235
## The loglikelihood after iter 374 is: -176984.835771
## The loglikelihood after iter 375 is: -177051.946691
## The loglikelihood after iter 376 is: -176981.463094
## The loglikelihood after iter 377 is: -176948.284834
## The loglikelihood after iter 378 is: -177006.786964
## The loglikelihood after iter 379 is: -176963.554625
## The loglikelihood after iter 380 is: -177134.526688
## The loglikelihood after iter 381 is: -176936.641898
## The loglikelihood after iter 382 is: -176921.677259
## The loglikelihood after iter 383 is: -177162.970084
## The loglikelihood after iter 384 is: -177088.620915
## The loglikelihood after iter 385 is: -176934.160847
## The loglikelihood after iter 386 is: -177115.072534
## The loglikelihood after iter 387 is: -176926.265296
## The loglikelihood after iter 388 is: -177057.416407
## The loglikelihood after iter 389 is: -177145.071384
## The loglikelihood after iter 390 is: -177258.980624
## The loglikelihood after iter 391 is: -177107.720755
## The loglikelihood after iter 392 is: -177074.551593
## The loglikelihood after iter 393 is: -177094.703113
## The loglikelihood after iter 394 is: -177183.552078
## The loglikelihood after iter 395 is: -177285.871055
## The loglikelihood after iter 396 is: -177193.646981
## The loglikelihood after iter 397 is: -177222.341392
## The loglikelihood after iter 398 is: -177146.196089
## The loglikelihood after iter 399 is: -177013.132214
## The loglikelihood after iter 400 is: -177233.893261
## The loglikelihood after iter 401 is: -177054.281476
## The loglikelihood after iter 402 is: -177121.198157
## The loglikelihood after iter 403 is: -177062.041823
## The loglikelihood after iter 404 is: -177114.481448
## The loglikelihood after iter 405 is: -177007.932464
## The loglikelihood after iter 406 is: -177030.065286
## The loglikelihood after iter 407 is: -176860.447484
## The loglikelihood after iter 408 is: -177124.518649
## The loglikelihood after iter 409 is: -177092.69712
## The loglikelihood after iter 410 is: -177062.00185
## The loglikelihood after iter 411 is: -176948.431756
## The loglikelihood after iter 412 is: -176953.250408
## The loglikelihood after iter 413 is: -176900.144456
## The loglikelihood after iter 414 is: -176955.356919
## The loglikelihood after iter 415 is: -176840.334487
## The loglikelihood after iter 416 is: -176896.576712
## The loglikelihood after iter 417 is: -177074.716389
## The loglikelihood after iter 418 is: -177037.516808
## The loglikelihood after iter 419 is: -176933.881778
## The loglikelihood after iter 420 is: -176993.272924
## The loglikelihood after iter 421 is: -176946.38447
## The loglikelihood after iter 422 is: -176945.943039
## The loglikelihood after iter 423 is: -176979.204476
## The loglikelihood after iter 424 is: -177100.939314
## The loglikelihood after iter 425 is: -177152.856244
## The loglikelihood after iter 426 is: -176977.60781
## The loglikelihood after iter 427 is: -177043.931554
## The loglikelihood after iter 428 is: -176955.790875
## The loglikelihood after iter 429 is: -176856.506422
## The loglikelihood after iter 430 is: -176985.81367
## The loglikelihood after iter 431 is: -176864.836927
## The loglikelihood after iter 432 is: -176972.58845
## The loglikelihood after iter 433 is: -176961.769443
## The loglikelihood after iter 434 is: -176894.048786
## The loglikelihood after iter 435 is: -176958.520458
## The loglikelihood after iter 436 is: -177064.77836
## The loglikelihood after iter 437 is: -176944.504861
## The loglikelihood after iter 438 is: -176988.305886
## The loglikelihood after iter 439 is: -177075.631295
## The loglikelihood after iter 440 is: -177159.011223
## The loglikelihood after iter 441 is: -176991.409125
## The loglikelihood after iter 442 is: -176880.964149
## The loglikelihood after iter 443 is: -176946.139644
## The loglikelihood after iter 444 is: -176944.830955
## The loglikelihood after iter 445 is: -176959.05801
## The loglikelihood after iter 446 is: -176912.042376
## The loglikelihood after iter 447 is: -176929.995453
## The loglikelihood after iter 448 is: -176935.243785
## The loglikelihood after iter 449 is: -176928.499701
## The loglikelihood after iter 450 is: -176919.964869
## The loglikelihood after iter 451 is: -176901.674027
## The loglikelihood after iter 452 is: -176924.424344
## The loglikelihood after iter 453 is: -176903.389289
## The loglikelihood after iter 454 is: -177006.55942
## The loglikelihood after iter 455 is: -176938.967154
## The loglikelihood after iter 456 is: -177016.754137
## The loglikelihood after iter 457 is: -177164.29263
## The loglikelihood after iter 458 is: -177167.837278
## The loglikelihood after iter 459 is: -177115.777697
## The loglikelihood after iter 460 is: -177213.742334
## The loglikelihood after iter 461 is: -177137.537146
## The loglikelihood after iter 462 is: -177044.653799
## The loglikelihood after iter 463 is: -177188.049546
## The loglikelihood after iter 464 is: -177151.578507
## The loglikelihood after iter 465 is: -176905.743267
## The loglikelihood after iter 466 is: -177256.532482
## The loglikelihood after iter 467 is: -177099.098461
## The loglikelihood after iter 468 is: -176877.965011
## The loglikelihood after iter 469 is: -177075.207632
## The loglikelihood after iter 470 is: -176982.699104
## The loglikelihood after iter 471 is: -177014.935387
## The loglikelihood after iter 472 is: -176940.126095
## The loglikelihood after iter 473 is: -176956.189265
## The loglikelihood after iter 474 is: -177122.760753
## The loglikelihood after iter 475 is: -176914.983101
## The loglikelihood after iter 476 is: -176990.362051
## The loglikelihood after iter 477 is: -177085.624658
## The loglikelihood after iter 478 is: -177117.206223
## The loglikelihood after iter 479 is: -177134.983215
## The loglikelihood after iter 480 is: -177139.520486
## The loglikelihood after iter 481 is: -177116.765643
## The loglikelihood after iter 482 is: -177088.99269
## The loglikelihood after iter 483 is: -176876.743261
## The loglikelihood after iter 484 is: -176944.343883
## The loglikelihood after iter 485 is: -176869.417662
## The loglikelihood after iter 486 is: -176836.570548
## The loglikelihood after iter 487 is: -176846.711992
## The loglikelihood after iter 488 is: -176763.776635
## The loglikelihood after iter 489 is: -176781.079695
## The loglikelihood after iter 490 is: -176774.091662
## The loglikelihood after iter 491 is: -176870.227188
## The loglikelihood after iter 492 is: -176821.408258
## The loglikelihood after iter 493 is: -176881.358408
## The loglikelihood after iter 494 is: -176946.695094
## The loglikelihood after iter 495 is: -176727.265023
## The loglikelihood after iter 496 is: -176886.665776
## The loglikelihood after iter 497 is: -176865.290557
## The loglikelihood after iter 498 is: -176898.667718
## The loglikelihood after iter 499 is: -176946.749466
## The loglikelihood after iter 500 is: -176857.257789## user system elapsed
## 1152.830 305.737 491.390library(plotrix)
library(RColorBrewer)
radial.plot(lengths=1:length(out_np$cell_times),radial.pos=out_np$cell_times[order(cell_times_reorder)],
line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(out_np$cell_times)), lwd=2)
radial.plot(lengths=1:length(cell_times_reorder),radial.pos=sort(cell_times_reorder),
line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(cell_times_reorder)), lwd=2)
The plots of estimated gene pattern and the true gene pattern.
First co-ordinate
plot(cycle_data_reorder[order(out_np$cell_times),1], type="l")
plot(cycle_data[,1],type="l")
30th coordinate
plot(cycle_data_reorder[order(out_np$cell_times),30], type="l")
plot(cycle_data[,30],type="l")
50th coordinate
plot(cycle_data_reorder[order(out_np$cell_times),50], type="l")
plot(cycle_data[,50],type="l")
Nonparametric cellcycleR : Wavelet method
system.time(out_np <- np_cell_ordering_class(cycle_data_reorder, celltime_levels = 256, num_iter=500, method="Wavelet"))## The loglikelihood after iter 1 is: -182423.767566
## The loglikelihood after iter 2 is: -178338.922768
## The loglikelihood after iter 3 is: -178129.284552
## The loglikelihood after iter 4 is: -177753.206386
## The loglikelihood after iter 5 is: -177791.562878
## The loglikelihood after iter 6 is: -178221.5473
## The loglikelihood after iter 7 is: -177923.453597
## The loglikelihood after iter 8 is: -178125.781374
## The loglikelihood after iter 9 is: -178028.119888
## The loglikelihood after iter 10 is: -178359.641468
## The loglikelihood after iter 11 is: -178097.614052
## The loglikelihood after iter 12 is: -178293.127096
## The loglikelihood after iter 13 is: -178465.260577
## The loglikelihood after iter 14 is: -177847.006297
## The loglikelihood after iter 15 is: -177842.594866
## The loglikelihood after iter 16 is: -177537.413663
## The loglikelihood after iter 17 is: -177199.200013
## The loglikelihood after iter 18 is: -176833.828967
## The loglikelihood after iter 19 is: -176135.159501
## The loglikelihood after iter 20 is: -175776.53056
## The loglikelihood after iter 21 is: -175880.396905
## The loglikelihood after iter 22 is: -175909.224798
## The loglikelihood after iter 23 is: -175961.255668
## The loglikelihood after iter 24 is: -175282.775339
## The loglikelihood after iter 25 is: -174249.690143
## The loglikelihood after iter 26 is: -174226.637903
## The loglikelihood after iter 27 is: -174240.484766
## The loglikelihood after iter 28 is: -174400.061331
## The loglikelihood after iter 29 is: -174511.913285
## The loglikelihood after iter 30 is: -174563.924638
## The loglikelihood after iter 31 is: -174663.939333
## The loglikelihood after iter 32 is: -174821.277124
## The loglikelihood after iter 33 is: -174983.866967
## The loglikelihood after iter 34 is: -175012.442625
## The loglikelihood after iter 35 is: -175255.057512
## The loglikelihood after iter 36 is: -175326.630292
## The loglikelihood after iter 37 is: -175524.329117
## The loglikelihood after iter 38 is: -175778.50388
## The loglikelihood after iter 39 is: -175531.57926
## The loglikelihood after iter 40 is: -175954.173205
## The loglikelihood after iter 41 is: -176043.854662
## The loglikelihood after iter 42 is: -175955.140762
## The loglikelihood after iter 43 is: -176060.666853
## The loglikelihood after iter 44 is: -176203.885801
## The loglikelihood after iter 45 is: -176158.715482
## The loglikelihood after iter 46 is: -176252.273956
## The loglikelihood after iter 47 is: -176280.464443
## The loglikelihood after iter 48 is: -176355.406318
## The loglikelihood after iter 49 is: -176677.625095
## The loglikelihood after iter 50 is: -176329.552631
## The loglikelihood after iter 51 is: -176495.819889
## The loglikelihood after iter 52 is: -176570.478935
## The loglikelihood after iter 53 is: -176708.494177
## The loglikelihood after iter 54 is: -176766.083145
## The loglikelihood after iter 55 is: -176832.580844
## The loglikelihood after iter 56 is: -177056.777036
## The loglikelihood after iter 57 is: -176944.990183
## The loglikelihood after iter 58 is: -177098.126165
## The loglikelihood after iter 59 is: -176938.545571
## The loglikelihood after iter 60 is: -176951.181408
## The loglikelihood after iter 61 is: -177146.726167
## The loglikelihood after iter 62 is: -176859.793333
## The loglikelihood after iter 63 is: -176754.658301
## The loglikelihood after iter 64 is: -176461.800091
## The loglikelihood after iter 65 is: -176080.713221
## The loglikelihood after iter 66 is: -175548.696214
## The loglikelihood after iter 67 is: -175226.574529
## The loglikelihood after iter 68 is: -175173.332349
## The loglikelihood after iter 69 is: -175180.186457
## The loglikelihood after iter 70 is: -175188.489763
## The loglikelihood after iter 71 is: -175222.734964
## The loglikelihood after iter 72 is: -175142.677669
## The loglikelihood after iter 73 is: -175084.79001
## The loglikelihood after iter 74 is: -175045.585011
## The loglikelihood after iter 75 is: -175003.590474
## The loglikelihood after iter 76 is: -175045.14709
## The loglikelihood after iter 77 is: -175103.208309
## The loglikelihood after iter 78 is: -175165.978109
## The loglikelihood after iter 79 is: -175377.954148
## The loglikelihood after iter 80 is: -175469.569649
## The loglikelihood after iter 81 is: -175657.881045
## The loglikelihood after iter 82 is: -176105.914403
## The loglikelihood after iter 83 is: -176398.262276
## The loglikelihood after iter 84 is: -176518.475676
## The loglikelihood after iter 85 is: -174891.626601
## The loglikelihood after iter 86 is: -174960.789801
## The loglikelihood after iter 87 is: -174899.237447
## The loglikelihood after iter 88 is: -175240.390296
## The loglikelihood after iter 89 is: -175161.369048
## The loglikelihood after iter 90 is: -175232.881163
## The loglikelihood after iter 91 is: -175395.920791
## The loglikelihood after iter 92 is: -175369.936276
## The loglikelihood after iter 93 is: -175546.891257
## The loglikelihood after iter 94 is: -175636.483671
## The loglikelihood after iter 95 is: -175792.141475
## The loglikelihood after iter 96 is: -176181.330332
## The loglikelihood after iter 97 is: -176036.751153
## The loglikelihood after iter 98 is: -176417.786173
## The loglikelihood after iter 99 is: -176280.202453
## The loglikelihood after iter 100 is: -176586.097899
## The loglikelihood after iter 101 is: -176958.813432
## The loglikelihood after iter 102 is: -176700.541941
## The loglikelihood after iter 103 is: -176528.442983
## The loglikelihood after iter 104 is: -176858.927764
## The loglikelihood after iter 105 is: -176434.092168
## The loglikelihood after iter 106 is: -176473.689639
## The loglikelihood after iter 107 is: -176991.994625
## The loglikelihood after iter 108 is: -176531.151658
## The loglikelihood after iter 109 is: -177240.368178
## The loglikelihood after iter 110 is: -177378.614656
## The loglikelihood after iter 111 is: -177045.996485
## The loglikelihood after iter 112 is: -177590.90331
## The loglikelihood after iter 113 is: -176836.254252
## The loglikelihood after iter 114 is: -177661.642936
## The loglikelihood after iter 115 is: -177287.480654
## The loglikelihood after iter 116 is: -177423.373229
## The loglikelihood after iter 117 is: -177428.685469
## The loglikelihood after iter 118 is: -177276.56945
## The loglikelihood after iter 119 is: -177039.14639
## The loglikelihood after iter 120 is: -177544.737706
## The loglikelihood after iter 121 is: -177527.362334
## The loglikelihood after iter 122 is: -177998.287844
## The loglikelihood after iter 123 is: -177223.277317
## The loglikelihood after iter 124 is: -177519.358033
## The loglikelihood after iter 125 is: -177443.231945
## The loglikelihood after iter 126 is: -177697.594654
## The loglikelihood after iter 127 is: -177488.62442
## The loglikelihood after iter 128 is: -177422.149706
## The loglikelihood after iter 129 is: -178057.358814
## The loglikelihood after iter 130 is: -177350.630397
## The loglikelihood after iter 131 is: -178292.206007
## The loglikelihood after iter 132 is: -177038.171344
## The loglikelihood after iter 133 is: -177596.961395
## The loglikelihood after iter 134 is: -177380.460338
## The loglikelihood after iter 135 is: -177248.814235
## The loglikelihood after iter 136 is: -177344.479753
## The loglikelihood after iter 137 is: -177279.568033
## The loglikelihood after iter 138 is: -177165.755305
## The loglikelihood after iter 139 is: -177455.437734
## The loglikelihood after iter 140 is: -177707.822019
## The loglikelihood after iter 141 is: -177091.401282
## The loglikelihood after iter 142 is: -178005.785391
## The loglikelihood after iter 143 is: -176896.559777
## The loglikelihood after iter 144 is: -177782.991252
## The loglikelihood after iter 145 is: -177177.453485
## The loglikelihood after iter 146 is: -176669.896591
## The loglikelihood after iter 147 is: -177416.357516
## The loglikelihood after iter 148 is: -176975.955923
## The loglikelihood after iter 149 is: -176942.379589
## The loglikelihood after iter 150 is: -177079.521529
## The loglikelihood after iter 151 is: -177020.773382
## The loglikelihood after iter 152 is: -177024.956778
## The loglikelihood after iter 153 is: -177438.84771
## The loglikelihood after iter 154 is: -177563.13683
## The loglikelihood after iter 155 is: -176822.765285
## The loglikelihood after iter 156 is: -177388.235459
## The loglikelihood after iter 157 is: -177801.327098
## The loglikelihood after iter 158 is: -176887.562418
## The loglikelihood after iter 159 is: -178025.49037
## The loglikelihood after iter 160 is: -176877.039749
## The loglikelihood after iter 161 is: -177277.114439
## The loglikelihood after iter 162 is: -177201.630483
## The loglikelihood after iter 163 is: -177079.458911
## The loglikelihood after iter 164 is: -177249.381527
## The loglikelihood after iter 165 is: -177160.990939
## The loglikelihood after iter 166 is: -177547.833245
## The loglikelihood after iter 167 is: -176831.241425
## The loglikelihood after iter 168 is: -176781.032549
## The loglikelihood after iter 169 is: -177249.437567
## The loglikelihood after iter 170 is: -176946.759423
## The loglikelihood after iter 171 is: -176462.111148
## The loglikelihood after iter 172 is: -176957.735741
## The loglikelihood after iter 173 is: -176947.355065
## The loglikelihood after iter 174 is: -176534.582682
## The loglikelihood after iter 175 is: -177152.46505
## The loglikelihood after iter 176 is: -176558.664413
## The loglikelihood after iter 177 is: -177386.666164
## The loglikelihood after iter 178 is: -176550.221975
## The loglikelihood after iter 179 is: -177023.287178
## The loglikelihood after iter 180 is: -176705.475397
## The loglikelihood after iter 181 is: -177670.787036
## The loglikelihood after iter 182 is: -176395.487231
## The loglikelihood after iter 183 is: -177531.603958
## The loglikelihood after iter 184 is: -176540.115446
## The loglikelihood after iter 185 is: -177250.686751
## The loglikelihood after iter 186 is: -176943.635085
## The loglikelihood after iter 187 is: -177070.322138
## The loglikelihood after iter 188 is: -177414.338888
## The loglikelihood after iter 189 is: -177034.597706
## The loglikelihood after iter 190 is: -176848.5919
## The loglikelihood after iter 191 is: -177720.126671
## The loglikelihood after iter 192 is: -176881.88387
## The loglikelihood after iter 193 is: -177053.543714
## The loglikelihood after iter 194 is: -177495.536118
## The loglikelihood after iter 195 is: -177182.996734
## The loglikelihood after iter 196 is: -176814.054998
## The loglikelihood after iter 197 is: -176613.407025
## The loglikelihood after iter 198 is: -177267.415885
## The loglikelihood after iter 199 is: -176131.584904
## The loglikelihood after iter 200 is: -176882.690361
## The loglikelihood after iter 201 is: -176720.549139
## The loglikelihood after iter 202 is: -177203.314772
## The loglikelihood after iter 203 is: -177198.730116
## The loglikelihood after iter 204 is: -177183.991746
## The loglikelihood after iter 205 is: -177585.441985
## The loglikelihood after iter 206 is: -176946.888725
## The loglikelihood after iter 207 is: -177266.983841
## The loglikelihood after iter 208 is: -177123.934303
## The loglikelihood after iter 209 is: -177487.550228
## The loglikelihood after iter 210 is: -177162.660593
## The loglikelihood after iter 211 is: -177213.298959
## The loglikelihood after iter 212 is: -177219.760962
## The loglikelihood after iter 213 is: -177537.74631
## The loglikelihood after iter 214 is: -177765.492416
## The loglikelihood after iter 215 is: -177092.43237
## The loglikelihood after iter 216 is: -177986.700277
## The loglikelihood after iter 217 is: -177294.354945
## The loglikelihood after iter 218 is: -177386.02921
## The loglikelihood after iter 219 is: -177508.163823
## The loglikelihood after iter 220 is: -177273.591884
## The loglikelihood after iter 221 is: -177647.143521
## The loglikelihood after iter 222 is: -177063.22311
## The loglikelihood after iter 223 is: -177228.138248
## The loglikelihood after iter 224 is: -177458.753231
## The loglikelihood after iter 225 is: -177239.285696
## The loglikelihood after iter 226 is: -177201.15003
## The loglikelihood after iter 227 is: -177467.524515
## The loglikelihood after iter 228 is: -177010.187837
## The loglikelihood after iter 229 is: -177858.405325
## The loglikelihood after iter 230 is: -176373.998077
## The loglikelihood after iter 231 is: -177509.837319
## The loglikelihood after iter 232 is: -176446.878114
## The loglikelihood after iter 233 is: -176858.829722
## The loglikelihood after iter 234 is: -176877.629782
## The loglikelihood after iter 235 is: -176782.493794
## The loglikelihood after iter 236 is: -176654.128279
## The loglikelihood after iter 237 is: -176628.19289
## The loglikelihood after iter 238 is: -176894.373178
## The loglikelihood after iter 239 is: -177023.184303
## The loglikelihood after iter 240 is: -176871.436456
## The loglikelihood after iter 241 is: -176625.259913
## The loglikelihood after iter 242 is: -177515.96722
## The loglikelihood after iter 243 is: -176410.689921
## The loglikelihood after iter 244 is: -177465.81356
## The loglikelihood after iter 245 is: -176498.386693
## The loglikelihood after iter 246 is: -176705.094847
## The loglikelihood after iter 247 is: -176534.145709
## The loglikelihood after iter 248 is: -176871.155648
## The loglikelihood after iter 249 is: -176857.065993
## The loglikelihood after iter 250 is: -177024.01575
## The loglikelihood after iter 251 is: -176683.317912
## The loglikelihood after iter 252 is: -177071.597086
## The loglikelihood after iter 253 is: -176689.931156
## The loglikelihood after iter 254 is: -177289.128656
## The loglikelihood after iter 255 is: -176592.891085
## The loglikelihood after iter 256 is: -177390.970063
## The loglikelihood after iter 257 is: -176656.700228
## The loglikelihood after iter 258 is: -177124.99025
## The loglikelihood after iter 259 is: -176651.698398
## The loglikelihood after iter 260 is: -176583.258846
## The loglikelihood after iter 261 is: -176492.827433
## The loglikelihood after iter 262 is: -176936.224915
## The loglikelihood after iter 263 is: -176583.310131
## The loglikelihood after iter 264 is: -176878.988945
## The loglikelihood after iter 265 is: -176483.662616
## The loglikelihood after iter 266 is: -176607.458902
## The loglikelihood after iter 267 is: -176737.275387
## The loglikelihood after iter 268 is: -177071.510694
## The loglikelihood after iter 269 is: -177366.691768
## The loglikelihood after iter 270 is: -177312.814822
## The loglikelihood after iter 271 is: -176822.733692
## The loglikelihood after iter 272 is: -177314.847501
## The loglikelihood after iter 273 is: -177246.427272
## The loglikelihood after iter 274 is: -177323.068513
## The loglikelihood after iter 275 is: -177268.496929
## The loglikelihood after iter 276 is: -177766.794367
## The loglikelihood after iter 277 is: -176637.355774
## The loglikelihood after iter 278 is: -177380.038964
## The loglikelihood after iter 279 is: -177442.18162
## The loglikelihood after iter 280 is: -177321.404361
## The loglikelihood after iter 281 is: -177597.321217
## The loglikelihood after iter 282 is: -177554.390191
## The loglikelihood after iter 283 is: -177724.409879
## The loglikelihood after iter 284 is: -177690.004767
## The loglikelihood after iter 285 is: -177568.328329
## The loglikelihood after iter 286 is: -176882.24896
## The loglikelihood after iter 287 is: -177119.851058
## The loglikelihood after iter 288 is: -176422.064044
## The loglikelihood after iter 289 is: -176859.54479
## The loglikelihood after iter 290 is: -176994.095341
## The loglikelihood after iter 291 is: -177670.026887
## The loglikelihood after iter 292 is: -176462.122999
## The loglikelihood after iter 293 is: -176942.654035
## The loglikelihood after iter 294 is: -176564.233622
## The loglikelihood after iter 295 is: -177030.576672
## The loglikelihood after iter 296 is: -177111.049854
## The loglikelihood after iter 297 is: -176636.253877
## The loglikelihood after iter 298 is: -176994.08033
## The loglikelihood after iter 299 is: -177382.464179
## The loglikelihood after iter 300 is: -176612.440578
## The loglikelihood after iter 301 is: -177234.823145
## The loglikelihood after iter 302 is: -177142.428195
## The loglikelihood after iter 303 is: -177330.569492
## The loglikelihood after iter 304 is: -176561.312629
## The loglikelihood after iter 305 is: -177227.950383
## The loglikelihood after iter 306 is: -176581.918568
## The loglikelihood after iter 307 is: -177153.975766
## The loglikelihood after iter 308 is: -176963.899972
## The loglikelihood after iter 309 is: -177744.19177
## The loglikelihood after iter 310 is: -176962.90633
## The loglikelihood after iter 311 is: -177660.439733
## The loglikelihood after iter 312 is: -177185.650357
## The loglikelihood after iter 313 is: -177509.017415
## The loglikelihood after iter 314 is: -177339.918795
## The loglikelihood after iter 315 is: -177289.638603
## The loglikelihood after iter 316 is: -177848.038183
## The loglikelihood after iter 317 is: -176731.439357
## The loglikelihood after iter 318 is: -177779.068867
## The loglikelihood after iter 319 is: -176266.856596
## The loglikelihood after iter 320 is: -177115.657453
## The loglikelihood after iter 321 is: -176942.400254
## The loglikelihood after iter 322 is: -177459.616089
## The loglikelihood after iter 323 is: -176788.331205
## The loglikelihood after iter 324 is: -177239.310294
## The loglikelihood after iter 325 is: -176717.401861
## The loglikelihood after iter 326 is: -177059.975679
## The loglikelihood after iter 327 is: -176549.685764
## The loglikelihood after iter 328 is: -177782.829835
## The loglikelihood after iter 329 is: -176711.133076
## The loglikelihood after iter 330 is: -177627.315552
## The loglikelihood after iter 331 is: -176854.370025
## The loglikelihood after iter 332 is: -177472.641573
## The loglikelihood after iter 333 is: -176623.910452
## The loglikelihood after iter 334 is: -177813.329047
## The loglikelihood after iter 335 is: -176170.123093
## The loglikelihood after iter 336 is: -177004.697105
## The loglikelihood after iter 337 is: -176142.706845
## The loglikelihood after iter 338 is: -176352.90681
## The loglikelihood after iter 339 is: -177064.913798
## The loglikelihood after iter 340 is: -176511.95586
## The loglikelihood after iter 341 is: -176909.450092
## The loglikelihood after iter 342 is: -176652.175885
## The loglikelihood after iter 343 is: -177138.037984
## The loglikelihood after iter 344 is: -177046.368139
## The loglikelihood after iter 345 is: -176481.516766
## The loglikelihood after iter 346 is: -176522.610595
## The loglikelihood after iter 347 is: -176803.635104
## The loglikelihood after iter 348 is: -177152.475873
## The loglikelihood after iter 349 is: -176972.790447
## The loglikelihood after iter 350 is: -177565.441136
## The loglikelihood after iter 351 is: -177133.016677
## The loglikelihood after iter 352 is: -177523.835772
## The loglikelihood after iter 353 is: -177661.990132
## The loglikelihood after iter 354 is: -176993.423013
## The loglikelihood after iter 355 is: -177919.998925
## The loglikelihood after iter 356 is: -177072.095045
## The loglikelihood after iter 357 is: -177453.131735
## The loglikelihood after iter 358 is: -177234.041955
## The loglikelihood after iter 359 is: -176728.938796
## The loglikelihood after iter 360 is: -177663.227246
## The loglikelihood after iter 361 is: -176918.188841
## The loglikelihood after iter 362 is: -177572.71933
## The loglikelihood after iter 363 is: -177030.856631
## The loglikelihood after iter 364 is: -177659.873655
## The loglikelihood after iter 365 is: -177283.833285
## The loglikelihood after iter 366 is: -177533.654111
## The loglikelihood after iter 367 is: -177412.712078
## The loglikelihood after iter 368 is: -177511.812019
## The loglikelihood after iter 369 is: -176936.584147
## The loglikelihood after iter 370 is: -177625.656122
## The loglikelihood after iter 371 is: -177061.885474
## The loglikelihood after iter 372 is: -176853.328709
## The loglikelihood after iter 373 is: -177073.339954
## The loglikelihood after iter 374 is: -177895.355658
## The loglikelihood after iter 375 is: -177033.989494
## The loglikelihood after iter 376 is: -177404.391777
## The loglikelihood after iter 377 is: -176956.305963
## The loglikelihood after iter 378 is: -177802.982767
## The loglikelihood after iter 379 is: -177094.094101
## The loglikelihood after iter 380 is: -177409.604995
## The loglikelihood after iter 381 is: -177304.742476
## The loglikelihood after iter 382 is: -177856.861339
## The loglikelihood after iter 383 is: -177553.336108
## The loglikelihood after iter 384 is: -177129.396718
## The loglikelihood after iter 385 is: -177470.904001
## The loglikelihood after iter 386 is: -177272.318458
## The loglikelihood after iter 387 is: -177135.703578
## The loglikelihood after iter 388 is: -177313.042193
## The loglikelihood after iter 389 is: -176896.802578
## The loglikelihood after iter 390 is: -177864.647355
## The loglikelihood after iter 391 is: -176291.416029
## The loglikelihood after iter 392 is: -177543.782279
## The loglikelihood after iter 393 is: -176751.499039
## The loglikelihood after iter 394 is: -176866.520273
## The loglikelihood after iter 395 is: -177091.585657
## The loglikelihood after iter 396 is: -176676.940589
## The loglikelihood after iter 397 is: -177216.49883
## The loglikelihood after iter 398 is: -176727.202676
## The loglikelihood after iter 399 is: -177132.418093
## The loglikelihood after iter 400 is: -177352.688536
## The loglikelihood after iter 401 is: -176973.649018
## The loglikelihood after iter 402 is: -177485.976809
## The loglikelihood after iter 403 is: -177084.04552
## The loglikelihood after iter 404 is: -176938.636111
## The loglikelihood after iter 405 is: -177572.828534
## The loglikelihood after iter 406 is: -177162.628512
## The loglikelihood after iter 407 is: -177983.932317
## The loglikelihood after iter 408 is: -177771.044829
## The loglikelihood after iter 409 is: -177559.412118
## The loglikelihood after iter 410 is: -178521.389216
## The loglikelihood after iter 411 is: -176872.71434
## The loglikelihood after iter 412 is: -177647.994071
## The loglikelihood after iter 413 is: -176852.991063
## The loglikelihood after iter 414 is: -177242.1113
## The loglikelihood after iter 415 is: -177437.600708
## The loglikelihood after iter 416 is: -177177.450259
## The loglikelihood after iter 417 is: -177349.761212
## The loglikelihood after iter 418 is: -177648.229234
## The loglikelihood after iter 419 is: -177410.903401
## The loglikelihood after iter 420 is: -177360.56981
## The loglikelihood after iter 421 is: -177281.470293
## The loglikelihood after iter 422 is: -178036.207928
## The loglikelihood after iter 423 is: -176669.303332
## The loglikelihood after iter 424 is: -177517.430299
## The loglikelihood after iter 425 is: -176730.303165
## The loglikelihood after iter 426 is: -177310.653563
## The loglikelihood after iter 427 is: -176776.284559
## The loglikelihood after iter 428 is: -177388.366966
## The loglikelihood after iter 429 is: -177077.056427
## The loglikelihood after iter 430 is: -176804.985975
## The loglikelihood after iter 431 is: -176888.189692
## The loglikelihood after iter 432 is: -177475.008103
## The loglikelihood after iter 433 is: -176794.326798
## The loglikelihood after iter 434 is: -177262.689984
## The loglikelihood after iter 435 is: -177132.476574
## The loglikelihood after iter 436 is: -177396.621847
## The loglikelihood after iter 437 is: -177738.001947
## The loglikelihood after iter 438 is: -177242.047774
## The loglikelihood after iter 439 is: -177583.827418
## The loglikelihood after iter 440 is: -177826.921268
## The loglikelihood after iter 441 is: -176595.732526
## The loglikelihood after iter 442 is: -176938.770645
## The loglikelihood after iter 443 is: -176920.072437
## The loglikelihood after iter 444 is: -176714.517263
## The loglikelihood after iter 445 is: -177367.468405
## The loglikelihood after iter 446 is: -176562.492781
## The loglikelihood after iter 447 is: -177173.832393
## The loglikelihood after iter 448 is: -177141.153947
## The loglikelihood after iter 449 is: -176872.525213
## The loglikelihood after iter 450 is: -177478.116686
## The loglikelihood after iter 451 is: -176713.564079
## The loglikelihood after iter 452 is: -176796.059874
## The loglikelihood after iter 453 is: -176691.261021
## The loglikelihood after iter 454 is: -176991.902942
## The loglikelihood after iter 455 is: -176932.626323
## The loglikelihood after iter 456 is: -176880.532609
## The loglikelihood after iter 457 is: -176851.098352
## The loglikelihood after iter 458 is: -176812.984538
## The loglikelihood after iter 459 is: -177085.115332
## The loglikelihood after iter 460 is: -177142.890633
## The loglikelihood after iter 461 is: -177242.406992
## The loglikelihood after iter 462 is: -177159.511293
## The loglikelihood after iter 463 is: -177282.681821
## The loglikelihood after iter 464 is: -177413.413385
## The loglikelihood after iter 465 is: -177450.223813
## The loglikelihood after iter 466 is: -176962.038235
## The loglikelihood after iter 467 is: -176825.604025
## The loglikelihood after iter 468 is: -176920.985474
## The loglikelihood after iter 469 is: -177408.540704
## The loglikelihood after iter 470 is: -176758.419883
## The loglikelihood after iter 471 is: -177078.360248
## The loglikelihood after iter 472 is: -176660.713366
## The loglikelihood after iter 473 is: -177035.882292
## The loglikelihood after iter 474 is: -176283.710506
## The loglikelihood after iter 475 is: -176902.218733
## The loglikelihood after iter 476 is: -176643.36238
## The loglikelihood after iter 477 is: -177233.209195
## The loglikelihood after iter 478 is: -176992.716194
## The loglikelihood after iter 479 is: -177010.797897
## The loglikelihood after iter 480 is: -177195.252313
## The loglikelihood after iter 481 is: -177571.77686
## The loglikelihood after iter 482 is: -177148.826516
## The loglikelihood after iter 483 is: -177022.714266
## The loglikelihood after iter 484 is: -176918.300693
## The loglikelihood after iter 485 is: -177111.537613
## The loglikelihood after iter 486 is: -176719.24624
## The loglikelihood after iter 487 is: -177727.660193
## The loglikelihood after iter 488 is: -176288.312888
## The loglikelihood after iter 489 is: -176957.156016
## The loglikelihood after iter 490 is: -177526.288724
## The loglikelihood after iter 491 is: -176823.685873
## The loglikelihood after iter 492 is: -177603.60806
## The loglikelihood after iter 493 is: -176689.43811
## The loglikelihood after iter 494 is: -177392.648564
## The loglikelihood after iter 495 is: -176997.057837
## The loglikelihood after iter 496 is: -177684.952608
## The loglikelihood after iter 497 is: -176600.49004
## The loglikelihood after iter 498 is: -177787.715737
## The loglikelihood after iter 499 is: -176268.354453
## The loglikelihood after iter 500 is: -177302.101683## user system elapsed
## 1127.810 314.480 466.723library(plotrix)
library(RColorBrewer)
radial.plot(lengths=1:length(out_np$cell_times),radial.pos=out_np$cell_times[order(cell_times_reorder)],
line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(out_np$cell_times)), lwd=2)
radial.plot(lengths=1:length(cell_times_reorder),radial.pos=sort(cell_times_reorder),
line.col=colorRampPalette(brewer.pal(9,"Blues"))(length(cell_times_reorder)), lwd=2)
The plots of estimated gene pattern and the true gene pattern.
First co-ordinate
plot(cycle_data_reorder[order(out_np$cell_times),1], type="l")
plot(cycle_data[,1],type="l")
30th coordinate
plot(cycle_data_reorder[order(out_np$cell_times),30], type="l")
plot(cycle_data[,30],type="l")
50th coordinate
plot(cycle_data_reorder[order(out_np$cell_times),50], type="l")
plot(cycle_data[,50],type="l")